When it comes to short read mapping there seemingly is no shortage of methods or software to choose from. Yet in practice we found that some published methods did now work at all, others exhibited suboptimal behaviors.
- What short read mappers do you use?
- How many reads do you need align and what is the size of the genome that you align to?
- What are the typical computational resources: parallel processes/CPU/memory required for the completion of the task?
- What is your overall assessment of the procedure: easy, tedious, fun?
Note: we're primarily looking to hear of your first hand, personal experiences with any given tool.
Anyone tried MUMmer (or MUMmergpu)?
Bill